BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= 011879
(475 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1XG2|A Chain A, Crystal Structure Of The Complex Between Pectin
Methylesterase And Its Inhibitor Protein
Length = 317
Score = 379 bits (974), Expect = e-105, Method: Compositional matrix adjust.
Identities = 175/305 (57%), Positives = 221/305 (72%)
Query: 169 GTGNFTKIMDAVLAAEDYSMKRFVIYIKRGVYKENVEIKKKKWNLMMVGDGIDATIISGN 228
GTG++ + +AV AA D S R+VIY+KRG YKENVE+ K NLM+VGDG+ AT I+G+
Sbjct: 11 GTGDYQTLAEAVAAAPDKSKTRYVIYVKRGTYKENVEVASNKMNLMIVGDGMYATTITGS 70
Query: 229 RNFMDGWTTFRSATFAVSGRGFIARDITFENTAGPEKHQAVALRSDSDLSVYFRCAIKGY 288
N +DG TTFRSAT A G+GFI +DI +NTAGP K QAVALR +D+SV RC I Y
Sbjct: 71 LNVVDGSTTFRSATLAAVGQGFILQDICIQNTAGPAKDQAVALRVGADMSVINRCRIDAY 130
Query: 289 QDSLYTHTMRQFFRECKISGTVDFIFGDATAMFQNCQILAKKGLDNQKNTITAHGRKDPN 348
QD+LY H+ RQF+R+ ++GTVDFIFG+A +FQ CQ++A+K Q+N +TA GR DPN
Sbjct: 131 QDTLYAHSQRQFYRDSYVTGTVDFIFGNAAVVFQKCQLVARKPGKYQQNMVTAQGRTDPN 190
Query: 349 EPTGFSIQFCNITADSDLLPFVNSTETYLGRPWKLYSRTVFMQSYMSNVIRPKGWLEWNN 408
+ TG SIQFCNI A SDL P + TYLGRPWK YSRTV M+SY+ +I P GW EW+
Sbjct: 191 QATGTSIQFCNIIASSDLEPVLKEFPTYLGRPWKEYSRTVVMESYLGGLINPAGWAEWDG 250
Query: 409 DFALDTLYYGEYKNYGPGGGLATRITWPGYHILNNAVQANNFTVAQFLEGNLWLPSTGVK 468
DFAL TLYYGE+ N GPG G + R+ WPGYH++ + +A FTVA+ ++G WL STGV
Sbjct: 251 DFALKTLYYGEFMNNGPGAGTSKRVKWPGYHVITDPAKAMPFTVAKLIQGGSWLRSTGVA 310
Query: 469 YTAGL 473
Y GL
Sbjct: 311 YVDGL 315
>pdb|1GQ8|A Chain A, Pectin Methylesterase From Carrot
Length = 319
Score = 347 bits (890), Expect = 8e-96, Method: Compositional matrix adjust.
Identities = 165/305 (54%), Positives = 212/305 (69%)
Query: 169 GTGNFTKIMDAVLAAEDYSMKRFVIYIKRGVYKENVEIKKKKWNLMMVGDGIDATIISGN 228
G+G++ + +AV AA + S R+VI IK GVY+ENV++ KKK N+M +GDG +TII+ +
Sbjct: 15 GSGDYKTVSEAVAAAPEDSKTRYVIRIKAGVYRENVDVPKKKKNIMFLGDGRTSTIITAS 74
Query: 229 RNFMDGWTTFRSATFAVSGRGFIARDITFENTAGPEKHQAVALRSDSDLSVYFRCAIKGY 288
+N DG TTF SAT A G GF+ARDITF+NTAG KHQAVALR SDLS ++RC I Y
Sbjct: 75 KNVQDGSTTFNSATVAAVGAGFLARDITFQNTAGAAKHQAVALRVGSDLSAFYRCDILAY 134
Query: 289 QDSLYTHTMRQFFRECKISGTVDFIFGDATAMFQNCQILAKKGLDNQKNTITAHGRKDPN 348
QDSLY H+ RQFF C I+GTVDFIFG+A + Q+C I A++ QKN +TA GR DPN
Sbjct: 135 QDSLYVHSNRQFFINCFIAGTVDFIFGNAAVVLQDCDIHARRPGSGQKNMVTAQGRTDPN 194
Query: 349 EPTGFSIQFCNITADSDLLPFVNSTETYLGRPWKLYSRTVFMQSYMSNVIRPKGWLEWNN 408
+ TG IQ I A SDL P +S TYLGRPWK YSRTV MQS ++NVI P GW W+
Sbjct: 195 QNTGIVIQKSRIGATSDLQPVQSSFPTYLGRPWKEYSRTVVMQSSITNVINPAGWFPWDG 254
Query: 409 DFALDTLYYGEYKNYGPGGGLATRITWPGYHILNNAVQANNFTVAQFLEGNLWLPSTGVK 468
+FALDTLYYGEY+N G G + R+TW G+ ++ ++ +A FT F+ G WL +T
Sbjct: 255 NFALDTLYYGEYQNTGAGAATSGRVTWKGFKVITSSTEAQGFTPGSFIAGGSWLKATTFP 314
Query: 469 YTAGL 473
++ GL
Sbjct: 315 FSLGL 319
>pdb|1QJV|A Chain A, Pectin Methylesterase Pema From Erwinia Chrysanthemi
pdb|1QJV|B Chain B, Pectin Methylesterase Pema From Erwinia Chrysanthemi
Length = 342
Score = 106 bits (265), Expect = 3e-23, Method: Compositional matrix adjust.
Identities = 95/309 (30%), Positives = 145/309 (46%), Gaps = 63/309 (20%)
Query: 173 FTKIMDAVLAAEDYSMKRFVIYIKRGVYKENVEIKKKKWNLMMVGDGIDATIISGNRNFM 232
F I DA+ +A S FVI IK GVY E + I + NL + G+ + +I+
Sbjct: 18 FKTIADAIASAPAGSTP-FVILIKNGVYNERLTITRN--NLHLKGESRNGAVIAAATAAG 74
Query: 233 ----DG--WTTFRSATFAVSGRGFIARDITFENTAGPEKHQAVALRSDSDLS-------- 278
DG W T S+T +S + F A+ +T N +QA +SDSD S
Sbjct: 75 TLKSDGSKWGTAGSSTITISAKDFSAQSLTIRNDFDFPANQA---KSDSDSSKIKDTQAV 131
Query: 279 ----------VYFR-CAIKGYQDSLYTHTMRQFFRECKISGTVDFIFGDATAMFQNCQIL 327
YF+ ++ GYQD+LY R FF +C+ISGTVDFIFGD TA+F NC ++
Sbjct: 132 ALYVTKSGDRAYFKDVSLVGYQDTLYVSGGRSFFSDCRISGTVDFIFGDGTALFNNCDLV 191
Query: 328 AKKGLDNQKNTITAH---GRKDPNEPTGFSIQFCNITADSDLLPFVNSTETY-LGRPW-- 381
++ D + ++ + + N+ G I + +SD +P ++Y LGRPW
Sbjct: 192 SRYRADVKSGNVSGYLTAPSTNINQKYGLVITNSRVIRESDSVP----AKSYGLGRPWHP 247
Query: 382 ------------KLYSRTVFMQSYMSNVIRPKGWLEWN-NDFALDTLYYG-------EYK 421
+TVF+ + M N I GW + + D +T+++ EYK
Sbjct: 248 TTTFSDGRYADPNAIGQTVFLNTSMDNHIY--GWDKMSGKDKNGNTIWFNPEDSRFFEYK 305
Query: 422 NYGPGGGLA 430
+YG G ++
Sbjct: 306 SYGAGAAVS 314
>pdb|2NTB|A Chain A, Crystal Structure Of Pectin Methylesterase In Complex With
Hexasaccharide V
pdb|2NTB|B Chain B, Crystal Structure Of Pectin Methylesterase In Complex With
Hexasaccharide V
pdb|2NTP|A Chain A, Crystal Structure Of Pectin Methylesterase In Complex With
Hexasaccharide Vi
pdb|2NTP|B Chain B, Crystal Structure Of Pectin Methylesterase In Complex With
Hexasaccharide Vi
pdb|2NTQ|A Chain A, Crystal Structure Of Pectin Methylesterase In Complex With
Hexasaccharide Vii
pdb|2NTQ|B Chain B, Crystal Structure Of Pectin Methylesterase In Complex With
Hexasaccharide Vii
Length = 342
Score = 105 bits (263), Expect = 4e-23, Method: Compositional matrix adjust.
Identities = 95/309 (30%), Positives = 145/309 (46%), Gaps = 63/309 (20%)
Query: 173 FTKIMDAVLAAEDYSMKRFVIYIKRGVYKENVEIKKKKWNLMMVGDGIDATIISGNRNFM 232
F I DA+ +A S FVI IK GVY E + I + NL + G+ + +I+
Sbjct: 18 FKTIADAIASAPAGSTP-FVILIKNGVYNERLTITRN--NLHLKGESRNGAVIAAATAAG 74
Query: 233 ----DG--WTTFRSATFAVSGRGFIARDITFENTAGPEKHQAVALRSDSDLS-------- 278
DG W T S+T +S + F A+ +T N +QA +SDSD S
Sbjct: 75 TLKSDGSKWGTAGSSTITISAKDFSAQSLTIRNDFDFPANQA---KSDSDSSKIKDTQAV 131
Query: 279 ----------VYFR-CAIKGYQDSLYTHTMRQFFRECKISGTVDFIFGDATAMFQNCQIL 327
YF+ ++ GYQD+LY R FF +C+ISGTVDFIFGD TA+F NC ++
Sbjct: 132 ALYVTKSGDRAYFKDVSLVGYQDTLYVSGGRSFFSDCRISGTVDFIFGDGTALFNNCDLV 191
Query: 328 AKKGLDNQKNTITAH---GRKDPNEPTGFSIQFCNITADSDLLPFVNSTETY-LGRPW-- 381
++ D + ++ + + N+ G I + +SD +P ++Y LGRPW
Sbjct: 192 SRYRADVKSGNVSGYLTAPSTNINQKYGLVITNSRVIRESDSVP----AKSYGLGRPWHP 247
Query: 382 ------------KLYSRTVFMQSYMSNVIRPKGWLEWN-NDFALDTLYYG-------EYK 421
+TVF+ + M N I GW + + D +T+++ EYK
Sbjct: 248 TTTFSDGRYADPNAIGQTVFLNTSMDNHIY--GWDKMSGKDKNGNTIWFNPEDSRFFEYK 305
Query: 422 NYGPGGGLA 430
+YG G ++
Sbjct: 306 SYGAGATVS 314
>pdb|2NSP|A Chain A, Crystal Structure Of Pectin Methylesterase D178a Mutant In
Complex With Hexasaccharide I
pdb|2NSP|B Chain B, Crystal Structure Of Pectin Methylesterase D178a Mutant In
Complex With Hexasaccharide I
pdb|2NST|A Chain A, Crystal Structure Of Pectin Methylesterase D178a Mutant In
Complex With Hexasaccharide Ii
pdb|2NST|B Chain B, Crystal Structure Of Pectin Methylesterase D178a Mutant In
Complex With Hexasaccharide Ii
pdb|2NT6|A Chain A, Crystal Structure Of Pectin Methylesterase D178a Mutant In
Complex With Hexasaccharide Iii
pdb|2NT6|B Chain B, Crystal Structure Of Pectin Methylesterase D178a Mutant In
Complex With Hexasaccharide Iii
pdb|2NT9|A Chain A, Crystal Structure Of Pectin Methylesterase D178a Mutant In
Complex With Hexasaccharide Iv
pdb|2NT9|B Chain B, Crystal Structure Of Pectin Methylesterase D178a Mutant In
Complex With Hexasaccharide Iv
Length = 342
Score = 102 bits (255), Expect = 4e-22, Method: Compositional matrix adjust.
Identities = 94/309 (30%), Positives = 144/309 (46%), Gaps = 63/309 (20%)
Query: 173 FTKIMDAVLAAEDYSMKRFVIYIKRGVYKENVEIKKKKWNLMMVGDGIDATIISGNRNFM 232
F I DA+ +A S FVI IK GVY E + I + NL + G+ + +I+
Sbjct: 18 FKTIADAIASAPAGSTP-FVILIKNGVYNERLTITRN--NLHLKGESRNGAVIAAATAAG 74
Query: 233 ----DG--WTTFRSATFAVSGRGFIARDITFENTAGPEKHQAVALRSDSDLS-------- 278
DG W T S+T +S + F A+ +T N +QA +SDSD S
Sbjct: 75 TLKSDGSKWGTAGSSTITISAKDFSAQSLTIRNDFDFPANQA---KSDSDSSKIKDTQAV 131
Query: 279 ----------VYFR-CAIKGYQDSLYTHTMRQFFRECKISGTVDFIFGDATAMFQNCQIL 327
YF+ ++ GYQ +LY R FF +C+ISGTVDFIFGD TA+F NC ++
Sbjct: 132 ALYVTKSGDRAYFKDVSLVGYQATLYVSGGRSFFSDCRISGTVDFIFGDGTALFNNCDLV 191
Query: 328 AKKGLDNQKNTITAH---GRKDPNEPTGFSIQFCNITADSDLLPFVNSTETY-LGRPW-- 381
++ D + ++ + + N+ G I + +SD +P ++Y LGRPW
Sbjct: 192 SRYRADVKSGNVSGYLTAPSTNINQKYGLVITNSRVIRESDSVP----AKSYGLGRPWHP 247
Query: 382 ------------KLYSRTVFMQSYMSNVIRPKGWLEWN-NDFALDTLYYG-------EYK 421
+TVF+ + M N I GW + + D +T+++ EYK
Sbjct: 248 TTTFSDGRYADPNAIGQTVFLNTSMDNHIY--GWDKMSGKDKNGNTIWFNPEDSRFFEYK 305
Query: 422 NYGPGGGLA 430
+YG G ++
Sbjct: 306 SYGAGATVS 314
>pdb|3UW0|A Chain A, Pectin Methylesterase From Yersinia Enterocolitica
Length = 364
Score = 94.7 bits (234), Expect = 1e-19, Method: Compositional matrix adjust.
Identities = 77/262 (29%), Positives = 113/262 (43%), Gaps = 48/262 (18%)
Query: 153 LLLVNGVQXXXXXXXXGTGNFTKIMDAVLAAEDYSMKRFVIYIKRGVYKENVEIKKKKWN 212
L VN Q G+ ++A L + F+I++K GVY E +E+ + +
Sbjct: 23 LGTVNAAQYNAVVSTTPQGDEFSSINAALKSAPKDDTPFIIFLKNGVYTERLEVARS--H 80
Query: 213 LMMVGDGIDATIISGNRNFM------DGWTTFRSATFAVSGRGFIARDITFENT------ 260
+ + G+ D T+I N + W T S+T V+ F A ++T N
Sbjct: 81 VTLKGENRDGTVIGANTAAGMLNPQGEKWGTSGSSTVLVNAPNFTAENLTIRNDFDFPAN 140
Query: 261 -----AGPEK---HQAVAL--RSDSDLSVYFRCAIKGYQDSLYTHT-MRQFFRECKISGT 309
P K QAVAL +SD + + ++GYQD+LY+ T R +F +C+ISG
Sbjct: 141 KKKADTDPTKLKDTQAVALLLAENSDKARFKAVKLEGYQDTLYSKTGSRSYFSDCEISGH 200
Query: 310 VDFIFGDATAMFQNCQILAKKGLDNQKNTITAHGRKDPNEPTGFSIQFCNITADSDLLPF 369
VDFIFG +F NC I+A+ R D P G+ +T L F
Sbjct: 201 VDFIFGSGITVFDNCNIVARD-------------RSDIEPPYGYITAPSTLTTSPYGLIF 247
Query: 370 VNSTET----------YLGRPW 381
+NS T LGRPW
Sbjct: 248 INSRLTKEPGVPANSFALGRPW 269
>pdb|3GRH|A Chain A, Crystal Structure Of Escherichia Coli Ybhc
Length = 422
Score = 37.0 bits (84), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 30/102 (29%), Positives = 40/102 (39%), Gaps = 16/102 (15%)
Query: 240 SATFAVSGRGFIARDITFENTAGPE----KHQAVALRSDSDLSVYFRCAIKGYQDSLYT- 294
SA F G +++T ENT G H AVALR+D D I G Q++ +
Sbjct: 193 SAVFWSQNNGLQLQNLTIENTLGDSVDAGNHPAVALRTDGDQVQINNVNILGRQNTFFVT 252
Query: 295 --------HTMRQ---FFRECKISGTVDFIFGDATAMFQNCQ 325
T RQ I G VD + G +F N +
Sbjct: 253 NSGVQNRLETNRQPRTLVTNSYIEGDVDIVSGRGAVVFDNTE 294
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.320 0.135 0.422
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,181,576
Number of Sequences: 62578
Number of extensions: 537201
Number of successful extensions: 985
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 973
Number of HSP's gapped (non-prelim): 11
length of query: 475
length of database: 14,973,337
effective HSP length: 102
effective length of query: 373
effective length of database: 8,590,381
effective search space: 3204212113
effective search space used: 3204212113
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (25.0 bits)